Are you running the batch file while the user is logged onto the machine? Normally, such user specific commands only work if that user is logged in. This is why the userobjs package parameter exists in order to stop packages with user dependent components being installed if the user is not logged in.

Yes, you can't edit the parameters in a channel.txt file in the same way that you can edit the tuner properties.txt/prefs.txt files. These are just externalised copies of the real files that are embedded in the tuner workspace itself. There is a channel called the workspace explorer floating around somewhere that lets you see the content of the current files in the workspace.